From 0f936f1e627bb7f9b152ae1d27f41c5bcaccb823 Mon Sep 17 00:00:00 2001 From: Taha Ahmed Date: Tue, 5 Apr 2011 17:49:15 +0200 Subject: [PATCH] Updated ocp2df() in CHI.R to put attributes in the dataframe columns. --- CHI.R | 50 ++++++++++++++++++++++++++++++++++---------------- common.R | 2 +- 2 files changed, 35 insertions(+), 17 deletions(-) diff --git a/CHI.R b/CHI.R index 769f144..951104a 100644 --- a/CHI.R +++ b/CHI.R @@ -18,10 +18,36 @@ source("/home/taha/chepec/chetex/common/R/common.R") ################### ocp2df ####################### ################################################## ocp2df <- function(datafilename) { - # Function description: for recorded amperometric i-T curves - # CH Instruments potentiostat records all data using standard SI units, - # so all potential values are in volts, currents are in amperes, - # charges in Coulombs, time in seconds, etc. + ## Description: + ## Reads potential-time data (from CHI 760 potentiostat) + ## and returns a dataframe with the data and + ## the data attributes (experimental conditions). + ## Usage: + ## ocp2df(datafilename) + ## Arguments: + ## datafilename: text string with full path to experimental file + ## Value: + ## Dataframe with the following columns (and no extra attributes): + ## $ sampleid : chr + ## $ time : num + ## $ current : num + ## $ currentdensity : num + ## $ timediff : num + ## $ dIdt : num + ## $ didt : num + ## $ charge : num + ## $ chargedensity : num + ## $ InitE : num + ## $ SampleInterval : num + ## $ RunTime : num + ## $ QuietTime : num + ## $ Sensitivity : num + ## Note: + ## The CH Instruments 760 potentiostat records all data + ## using standard SI units, therefore this function + ## assumes all potential values to be in volts, + ## currents to be in amperes, charges in Coulombs, + ## time in seconds, and so on. # datafile <- file(datafilename, "r") chifile <- readLines(datafile, n = -1) #read all lines of input file @@ -63,18 +89,10 @@ ocp2df <- function(datafilename) { names(ff) <- c("sampleid", "time", "potential") # ### Collect attributes of this experiment - # These attributes are specific for each kind of experiment, - # be careful when adapting to other electrochemical data - rgxp.attr <- c("^Run\\sTime\\s\\(sec\\)") - names.attr <- c("RunTime") - for (n in 1:length(rgxp.attr)) { - attrow.idx <- regexpr(rgxp.attr[n], chifile) - attrow.len <- attr(attrow.idx, "match.length") - attr(attrow.idx, "match.length") <- NULL - # attrow.idx should now contain only one matching row - attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)], - "\\s=\\s")[[1]][2] - } + # RunTime (sec) + position.RunTime <- regexpr("^Run\\sTime\\s\\(sec\\)", chifile) + RunTime <- as.numeric(strsplit(chifile[which(position.RunTime == 1)], "\\s=\\s")[[1]][2]) + ff$RunTime <- RunTime # return(ff) } diff --git a/common.R b/common.R index 31691d5..7bf220f 100644 --- a/common.R +++ b/common.R @@ -5,7 +5,7 @@ # CONTENTS # >>>> LinearBaseline (deprecated) # >>>> int2padstr -# >>>> It2charge +# >>>> It2charge **** STOP USING THIS FUNCTION *** # >>>> ProvideSampleId # >>>> ConvertRefPot # >>>> Celsius2Kelvin